Re: [AMBER] MMGBSA on Protein-DNA/RNA complex

From: Vlad Cojocaru <>
Date: Wed, 24 Jun 2015 15:21:40 +0200

The default ipb is 2, not 1 ... We did not change this default.

However, lots of PBSA parameters set by default by the script
are not suitable for the calculations discussed in this thread (at least
in Amber Tools 14, I did not do calculations yet with the 15 version).
Because of this I'd advise you to follow Jason's advice "to set
use_sander=1 and then use the -make-mdins and -use-mdins flags to modify
the sander mdin files directly". In fact, should you wish to follow the
protocol we used in the Structure paper, you'll need to do that ...

Below you have an example input file you may start with. But please
document yourself on every single parameter set in there before running
massive calculations. Moreover, please note that if you change one
parameter, others may be affected to. So, you really need to understand
what you are doing.


MMPBSA, Nonlinear PB, inp=2, sasopt=2
  nsnb=99999, dec_verbose=0, ioutfm=1,
  ipb=2, ntb=0, cut=999.0, imin=5,
  igb=10, inp=2,
  epsin=4, epsout=80, smoothopt=1,
  istrng=100.0, pbtemp=300, radiopt=1,
  dprob=1.4, iprob=2.0, sasopt=2, saopt=0,
  triopt=1, arcres=0.25,
  npbopt=1, solvopt=1, accept=0.001,
  maxitn=100, fillratio=4.0, space=0.5,
  nbuffer=0, nfocus=2, fscale=8, npbgrid=1,
  bcopt=5, eneopt=1, frcopt=0, scalec=0,
  cutfd=5.0, cutnb=12, nsnba=1,
  decompopt=2, use_rmin=1, sprob=0.557, vprob=1.3,
  rhow_effect=1.129, use_sav=1,
  cavity_surften=0.0378, cavity_offset=-0.5692,

On 06/24/2015 02:27 PM, Jason Swails wrote:
> On Wed, Jun 24, 2015 at 4:02 AM, Muthukumaran R <>
> wrote:
>> I tried MMPBSA, with following input on amber tools 14 (AMBER12)
>> Sample input file with pb analysis
>> &general
>> startframe=15000, endframe=20000,interval=50,
>> verbose=2, keep_files=1,
>> /
>> &pb
>> istrng=0.1, indi=4, scale=2, inp=2,
>> /
>> when I included the option "ipb=1" in &general or &pb, it gives the same
>> error
>> InputError: Unknown variable ipb in &pb.
> ​ makes no use of the ipb variable. It is automatically set to 1
> in the sander or mmpbsa_py_energy input files. If you want to change this
> value to something *besides* 1, you probably need to set use_sander=1 and
> then use the -make-mdins and -use-mdins flags to modify the sander mdin
> files directly. If the value of 1 suffices (as it usually does), just omit
> ipb altogether.
> For pure energies, I don't think the value of ipb will make much of a
> difference. If you're doing dynamics with PB, then the functional form of
> the dielectric boundary matters since you're computing gradients. But if
> you're just computing solvation free energies, I doubt it will have a very
> noticeable effect (hopefully someone can correct me if I'm misunderstanding
> this).
> HTH,
> Jason

Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]
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Received on Wed Jun 24 2015 - 06:30:02 PDT
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